Manuscript Contents & Organization

Preparing the Manuscript Text

Authors should prepare their manuscript as a single PDF file (including figures). For initial submission, the primary goal is for the manuscript to contain the necessary informationto enable a full scientific assessment; so while all sections of the manuscript need to be present, references need to be complete, and figures and tables need to be clearly numbered, adherence to the remaining formatting guidelines described below is not critical. Revised manuscripts, however, must adopt MCP's style below to avoid delays in review or publication. Authors must always follow MCP’s data reporting requirements for protein identification and other relevant guidelines to avoid complications in submission and review.

Formatted for an 8.5 x 11 page

Double spacing throughout

One-inch margins

Text in a font size of at least 10 points

Number all pages including figures beginning with the title page as page 1

Tables (Supplemental tables and their legends should not be included in the main article PDF)

Figures and Figure Legends (Supplemental figures and their legends should not be included in the main article PDF)

Title

As short and informative as possible.

Should be intelligible to MCP readers who are not specialists in the field and should convey your essential points clearly.

Should not exceed two printed lines.

Acronyms or abbreviations may be used without definition in the title, but authors should strive to limit abbreviations for clarity. Any abbreviations that do not appear on this list of common terms should be defined at first usage in the abstract or main text.

Authors

Should include the complete names of all authors and affiliations where the work was performed (for those authors who have since moved, please indicate their present address as a separate note).

Should identify which author will receive correspondence regarding the manuscript and include this author’s telephone number and current e-mail address.

Running Title

Should be at the top of each page except the first, where it should appear below the author affiliations.

Cannot exceed 60 characters and spaces.

Abbreviations

All abbreviations are to be listed and defined. A list of abbreviations not requiring definition can be found here.

Abbreviations in the title do not need to be defined within the title; define them (if necessary, see next) at their first appearance in the abstract or main text.

Numerical data should be reported with the number of significant digits that corresponds to the magnitude of experimental uncertainty.

Compounds: The rules and recommendations of IUPAC should be used for abbreviation of chemical names, nomenclature of chemical compounds, isotopic compounds, optically active isomers, and spectroscopic data; more information can be found here.

Enzymes: The trivial and systematic names of enzymes should be those recommended by the Nomenclature Committee of the IUBMB and not abbreviated except in terms of the substrates for which there are accepted abbreviations — e.g., ATPase and RNase.

Organisms: Nomenclature should follow the guidelines developed by the American Society for Microbiology.

Lipids: The use of the classification, nomenclature and structural representation of lipids used by the LIPID MAPS Initiative should be used whenever possible (see Fahy et al. (2005) J. Lipid Res. 46, 839–862 and Fahy et al. (2009) J. Lipid Res. 50, S9–S14). Lipid structures can be downloaded directly from the “Lipid Classification” section of the LIPID MAPS Web site or structures drawn de novo from the “Tools” section of the website, and then inserted into the manuscript.

Glycans: All figures that depict glycans using symbols for monosaccharides should follow the shapes and colors presented in the current version of the Symbol Nomenclature for Glycans (SNFG). The original citation is Varki et al. (2015) Glycobiology 25, 1323–1324

If the manuscript includes human or animal studies, authors must include a statement as to whether the studies were approved and by which review board. Please also see our Clinical Proteomics Guidelines for data that were obtained from human tissues/fluids (except for cell lines not established as part of the reported study).

Can be abbreviated or combined with Results in technology papers

Results

Presented in figures and tables

Some results not requiring documentation given solely in the text

Extensive discussion not in Results section

Discussion

Concise interpretation

Focused on the interpretation of results rather than a repetition of the Results section

Acknowledgments

Funding sources. As of October 27, 2015 it is the responsibility of all corresponding authors of NIH supported papers to include the required disclaimer in a footnote: The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Farrell, C. (1992) The Role of SecB during Protein Export in Escherichia coli. Ph.D. thesis, The Johns Hopkins University

Unpublished observations and personal communications

Must be cited using footnotes.

Written approval for all personal communications, exactly as written in the text, should be available upon request.

Tables

Should have an overall title and each column within the table must have a heading.

Should contain sufficient experimental detail to be understood without reference to the text.

Abbreviations, when necessary, should be defined in the legend.

Complex tables, such as sequence alignments, should be submitted as figures. Very large tables that cannot fit on a single page (e.g., peptide/protein identification data by mass spectrometry) should be submitted as Supplemental Data in an appropriate format such as Excel.

Figures and Figure Legends

Figures and legends should both appear at the end of the PDF (not placed within the body text of the manuscript)

Legends should contain sufficient detail to make the figure easily understood.

Legends should appear underneath the figures to which they refer.

Should be numbered in the order in which they are mentioned in the text.

All symbols should be defined and all equations used to plot lines and curves should be provided.

See below for more instructions on preparing figures.

Preparing Figures

The initial submission of both text and figures for peer review should be as a single PDF file. It is the authors' responsibility to review the accuracy of figures in the PDF file before submission. Authors should create figures using applications that are capable of preparing high resolution TIFF or EPS file formats. Even though figures will be in PDF format for initial submission, we will require submission of figures as separate TIFF or EPS files at publication quality resolution upon acceptance. Important information on the preparation of figures in TIFF or EPS, can be found here.

Figures

Numbered figures should be included at the end of the combined manuscript file. Tips on how to prepare these files can be found here. Figures supplied in EPS format should have all fonts converted to outlines/paths to avoid problems with character substitutions (in Adobe Illustrator, choose Edit > Select All then Type > Create Outlines).

It is the authors’ responsibility to verify the quality of the graphics and confirm that compression of the files during the submission process does not distort the images.

Color figures must be prepared in RGB color mode, not CMYK. The use of color figures is encouraged where they will enhance the presentation of the data. Any figure submitted in color will be reviewed and processed with the understanding that the figure will be published in color.

Figure dimensions and labeling

Figure files should be properly sized and cropped so that no unnecessary white space is left bordering the figure. Figures will be placed in 1 (3.5 in/8.9 cm), 1.5 (5 in/12.7 cm) or 2 (7.2 in/18.2 cm) column widths. The maximum height is 6 inches (15 cm). Panels should be assembled into a single composite figure that fits on one page and this image saved as a single file.

Text labels should be adjusted so that the smallest type on the figure will be at least 2mm at the intended width. The sizes of numbers, letters and symbols used in multi-paneled figures should be consistent between panels and units of measurement must be given. Helvetica or European PI fonts should be used for best results.

Image resolution

Figures must be prepared with the proper resolution for publication to avoid inaccurate presentation of the data. The minimum acceptable resolution for all figures is 300 dpi. Excessive file compression can distort images, so files should be carefully checked after compression. Note that figures that contain both line art (such as graphs) and RGB/grayscale areas (such as photographs) are best prepared as EPS (vector) files with embedded TIFF images for the RGB/grayscale portions. The resolution of those embedded TIFF images should be at least 300 dpi.

If you require further information, please send an e-mail query to mcp@asbmb.org.

Supplemental Data

All the data necessary to support the conclusions of a paper should be included with the main body of the paper. Any additional data supporting the research reported in a manuscript but not essential for the interpretations presented in the text may be included as Supplemental Data. Also, data in formats that cannot be accommodated in the text may be included as Supplemental Data. Therefore, Supplemental Data may include: extensive mass spectrometry data, experimental results under additional conditions, non-essential controls, videos, 3-D structures/images, extended chemical syntheses, kinetic modeling data, and other large data sets.

Supplemental Data will be reviewed as a part of the normal manuscript review process and will be judged by the same rigorous criteria as the main body of the paper. Most Supplemental Data (except for large supplemental tables) can be submitted as a single pdf file; this pdf should begin with the title of the article, the names of the authors, and a list of the material included. Pages should be numbered S-1, S-2 and so forth. Tables and figures in Supplemental Data should be labeled Table S1, Table S2 and so forth. Each figure legend should be placed directly by the figure. If references are used in this section, a list should be placed at the end. All supporting tables and figures must be of high quality. Supplemental Data in file types other than pdf, such as large data files, movies, etc., should be submitted in their native formats as separate files, and the content listed/described in the main Supplemental Data pdf. Protein and peptide identification data using mass spectrometry such as those required in our guidelines should be provided in Excel format to allow easy examination of the data. Supplemental Data cannot be added after acceptance.

Supplemental Data should not contain preliminary data that simply extends the scope of the study, unnecessary "control" data, or data that are thought to be not "clean enough" for the main text. Some detailed methodology may be presented in the Supplemental Data, but it should not be viewed as a "dump" for most methods; the main text should contain sufficient methodology for an experienced investigator to replicate the experiments. Authors should carefully review the Supplementary Data for factual, grammatical, and typographical issues since this material will not be professionally copyedited but permanently posted "as is".

Source files for supplemental data are NOT needed at the time of acceptance. We will use the files included in your submission. Supplemental files cannot be added after acceptance.

Resubmissions

Revised manuscripts must be accompanied by a cover letter that includes a detailed point-by-point response listing as to how each of the reviewers’ comments has been addressed and describes any other changes made to the manuscript. Authors are invited to upload a copy of the original manuscript marked using Word with Track Changes, highlighting, or colored text to indicate changes and facilitate evaluation of the revisions. Such a file should be uploaded as “Supplemental Data (for reviewers only),” so that it does not appear online if this version of the paper is accepted. The main PDF file should not include tracked changes/color, etc., and should follow the formatting requirements as described above as it will be published directly as a Paper in Press if accepted. In addition, all resubmissions must be accompanied by Graphical Abstract, Highlights and In Brief for use in publication (see below for more detail).

Graphical Abstract, Highlights, and In Brief

All authors submitting a revised/resubmitted manuscript must also provide a graphical abstract, highlights, and in brief statement.Authors of new papers are also encouraged to submit these files; they are optional on initial submission. The graphical abstract is an image that is displayed on the first page of the article PDF, along with “In Brief” and “Highlight”. It will also be prominently displayed online on the MCP website in both the Table of Contents and the article page view.

The graphical abstract is intended to be the first landing page for readers to give them an immediate impression of the primary message of the paper. It is designed to help readers easily identify papers that are most relevant to their research interests.

Size: The submitted image should be 4.4x3.6 inches (1320x1080 pixels) at 300 dpi.Font: Arial, 14–16 points. Smaller fonts will not be legible.Preferred file types: TIFF, JPGContent: the graphical abstract should consist of one single panel; you may reuse elements from figures in the paper

During revision/resubmission: on the eJournalPress page where you are asked to upload your files, please choose "Graphical Abstract" and upload a single image file (TIFF or JPG) for your graphical abstract.

The graphical abstract should:

Consist of one single panel diagram

Must be a new figure not included in the paper itself; however, we would accept an adapted figure from the paper as long as it captures all the salient points of a graphical abstract

Have a clear direction, start and end, "reading" from top‐to‐bottom or left‐to‐right

Provide a visual indication of the biological or technological context of the results depicted (subcellular location, tissue or cell type, species, etc.)

Emphasize the new findings from the current paper without including excess details from previous literature

Avoid the inclusion of features that are more speculative (unless the speculative nature can be made apparent visually)

Not include data items of any type; all the content should be in a graphical form

Use simple labels and minimal text

Font size of any labels and text must be of a sufficient size to be clear and easily legible upon figure reduction to fit page

Highlight one process or make one point clear

Be free of distracting and cluttering elements

Use colors effectively to enhance the graphical abstract both aesthetically and by directing the reader's attention to focal points of interest

Highlights and In Brief Statement

Highlights are bullet points that convey the core findings of your paper. You may include up to four highlights. The length of each highlight cannot exceed 85 characters (including spaces).

The “In Brief” blurb is a short summary that describes the context and significance of the findings for the broader readership, which is displayed within an issue’s Table of Contents. The blurb should be 80 words or less.

During revision/resubmission: on the eJournalPress page where you are asked to upload your files, please choose "Highlights and In Brief" and upload a single Word document containing both items.

Mechanistic insights into two high-grade astrocytomas from proteomes and PTMs

In Brief
The proteomes, phosphoproteomes and histone PTM occupancies have been determined for HRAS and mutant IDH1 driven glioma cells by applying quantitative MS-based proteomics. These cell lines mimick primary and secondary high-grade astrocytoma, respectively. The results reported reveal driving roles of the MEK and PI3K signaling pathways and provide a quantitative view of major effects of the oncometabolite, 2-hydroxyglutarate, on histone PTM occupancies.